Variant report

Variant	rs1405209
Chromosome Location	chr9:102585545-102585546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:102585214-102585700	PFSK-1	brain:	n/a	n/a
2	STAT5A	chr9:102585094-102585884	GM12878	blood:	n/a	chr9:102585524-102585535 chr9:102585098-102585106
3	POLR2A	chr9:102581488-102585733	GM19193	blood:	n/a	n/a
4	CEBPB	chr9:102584987-102585809	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr9:102583087-102585689	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr9:102585440-102585590	GM12864	blood:	n/a	n/a
7	TCF12	chr9:102585038-102585801	A549	lung:	n/a	n/a
8	MAX	chr9:102584958-102585618	SK-N-SH	brain:	n/a	chr9:102585006-102585015
9	CTBP2	chr9:102583360-102585712	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr9:102583007-102585793	GM12878	blood:	n/a	chr9:102584606-102584614 chr9:102583379-102583390
11	PAX5	chr9:102585244-102585778	GM12878	blood:	n/a	n/a
12	MXI1	chr9:102580459-102586751	SK-N-SH	brain:	n/a	chr9:102585006-102585021
13	MAX	chr9:102581551-102585861	Hela-S3	cervix:	n/a	chr9:102582833-102582843 chr9:102583341-102583348 chr9:102582184-102582194 chr9:102581879-102581888 chr9:102585006-102585015
14	HCFC1	chr9:102581313-102586195	Hela-S3	cervix:	n/a	n/a
15	SMARCB1	chr9:102583266-102585796	Hela-S3	cervix:	n/a	n/a
16	EP300	chr9:102584666-102585606	ECC-1	luminal epithelium:	n/a	n/a
17	MTA3	chr9:102584995-102585893	GM12878	blood:	n/a	n/a
18	MXI1	chr9:102582345-102587220	IMR90	lung:	n/a	chr9:102585006-102585021
19	POLR2A	chr9:102580651-102615596	IMR90	lung:	n/a	n/a
20	RAD21	chr9:102582378-102585874	IMR90	lung:	n/a	chr9:102584037-102584047 chr9:102584036-102584050 chr9:102584561-102584575 chr9:102584462-102584472
21	MAX	chr9:102585048-102585826	SK-N-SH	brain:	n/a	n/a
22	TCF7L2	chr9:102581544-102585806	Hela-S3	cervix:	n/a	chr9:102582536-102582543
23	RUNX3	chr9:102585101-102585711	GM12878	blood:	n/a	n/a
24	RUNX3	chr9:102585075-102585636	GM12878	blood:	n/a	n/a
25	RFX5	chr9:102585073-102585637	Hela-S3	cervix:	n/a	n/a
26	RCOR1	chr9:102581431-102585931	Hela-S3	cervix:	n/a	n/a
27	SUZ12	chr9:102584043-102587959	NT2-D1	testis:	n/a	n/a
28	CHD2	chr9:102583139-102586010	Hela-S3	cervix:	n/a	n/a
29	SIN3AK20	chr9:102581374-102585930	MCF-7	breast:	n/a	n/a
30	MAX	chr9:102585145-102585599	K562	blood:	n/a	n/a
31	MYC	chr9:102585321-102585774	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr9:102585080-102585625	Hela-S3	cervix:	n/a	n/a
33	TBP	chr9:102585120-102585985	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr9:102585162-102585584	GM12891	blood:	n/a	n/a
35	MXI1	chr9:102581490-102585550	GM12878	blood:	n/a	chr9:102585006-102585021
36	CTCF	chr9:102585440-102585590	GM12873	blood:	n/a	n/a
37	MAX	chr9:102584997-102585651	ECC-1	luminal epithelium:	n/a	chr9:102585006-102585015
38	WRNIP1	chr9:102585201-102585675	GM12878	blood:	n/a	n/a
39	POLR2A	chr9:102583054-102585623	HL-60	blood:	n/a	n/a
40	POLR2A	chr9:102584985-102585588	Hela-S3	cervix:	n/a	n/a
41	MAX	chr9:102585481-102585681	HepG2	liver:	n/a	n/a
42	CTCF	chr9:102585420-102585570	GM12865	blood:	n/a	n/a
43	PAX5	chr9:102585392-102585661	GM12878	blood:	n/a	n/a
44	SMC3	chr9:102583188-102585583	Hela-S3	cervix:	n/a	chr9:102584462-102584472
45	MAZ	chr9:102585071-102586330	Hela-S3	cervix:	n/a	n/a
46	SIN3A	chr9:102581403-102585906	H1-hESC	embryonic stem cell:	n/a	chr9:102581864-102581877 chr9:102581893-102581906 chr9:102584606-102584614 chr9:102583379-102583390
47	MXI1	chr9:102584952-102585656	Hela-S3	cervix:	n/a	chr9:102585006-102585021
48	GTF2F1	chr9:102585100-102585713	Hela-S3	cervix:	n/a	n/a
49	E2F6	chr9:102584951-102585741	A549	lung:	n/a	chr9:102585093-102585107 chr9:102585092-102585107
50	MYC	chr9:102585181-102585584	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:101983020..101985403-chr9:102581774..102586122,4	MCF-7	breast:
2	chr9:102584673..102587915-chr9:102597686..102600720,3	MCF-7	breast:
3	chr9:102580555..102587852-chr9:102667958..102670918,11	MCF-7	breast:
4	chr9:102580482..102589062-chr9:102666380..102672134,16	MCF-7	breast:
5	chr9:102584341..102585934-chr9:102646310..102647874,2	MCF-7	breast:
6	chr21:44840840..44841677-chr9:102585371..102586023,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000237461	TF binding region
NR4A3	TF binding region
ENSG00000255145	Chromatin interaction
ENSG00000106803	Chromatin interaction
ENSG00000119523	Chromatin interaction
ENSG00000136874	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10156557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988895	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988904	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988905	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336436	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1417738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918734	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918009	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965564	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900222	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742773	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742774	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019989	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029504	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029559	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038780	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041475	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744685	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893621	chr9:102342950-102585545	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv893622	chr9:102543355-102595685	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1405209	C9orf125	cis	parietal	SCAN
rs1405209	PPP3R2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102580800-102586800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:102581000-102585600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:102581000-102586400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:102581200-102585600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:102581200-102586200	Active TSS	Hela-S3	cervix
6	chr9:102581200-102587200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr9:102581200-102587200	Active TSS	NHDF-Ad	bronchial
8	chr9:102581200-102587400	Active TSS	Psoas Muscle	Psoas
9	chr9:102581200-102587800	Active TSS	NHLF	lung
10	chr9:102581400-102586400	Active TSS	Brain Cingulate Gyrus	brain
11	chr9:102581400-102586600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:102581400-102586600	Active TSS	Left Ventricle	heart
13	chr9:102581400-102586600	Active TSS	Ovary	ovary
14	chr9:102581400-102586800	Active TSS	Aorta	Aorta
15	chr9:102581400-102586800	Active TSS	Colon Smooth Muscle	Colon
16	chr9:102581400-102587000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:102581400-102587000	Active TSS	A549	lung
18	chr9:102581400-102587200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:102581400-102587200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:102581400-102587400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr9:102581600-102586200	Active TSS	Lung	lung
22	chr9:102581600-102586400	Active TSS	Brain Anterior Caudate	brain
23	chr9:102581600-102586600	Active TSS	Brain Hippocampus Middle	brain
24	chr9:102581600-102586600	Active TSS	Gastric	stomach
25	chr9:102581800-102589800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:102582400-102585800	Flanking Bivalent TSS/Enh	Dnd41	blood
27	chr9:102582400-102586600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
28	chr9:102582600-102585800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:102582600-102588000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:102583000-102588200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr9:102583200-102585600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:102583200-102586400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:102583200-102586400	Active TSS	HSMM	muscle
34	chr9:102583400-102586600	Active TSS	Fetal Heart	heart
35	chr9:102583600-102587200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:102583600-102587400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr9:102584200-102585800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
38	chr9:102584200-102586000	Flanking Active TSS	HUVEC	blood vessel
39	chr9:102584200-102586600	Flanking Active TSS	Liver	Liver
40	chr9:102584200-102587400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
41	chr9:102584400-102585800	Flanking Active TSS	HMEC	breast
42	chr9:102584400-102586000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:102584400-102586000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
44	chr9:102584400-102586000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr9:102584400-102586600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
46	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
49	chr9:102584400-102587600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
50	chr9:102584400-102587600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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